BN1206 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 5.3812e-07 2.5506e-03
Layer 4 1.7573e-06 3.9852e-05
Layer 2 4.1292e-06 1.0303e-03
Layer 6 2.9621e-05 9.5307e-03
Layer 5 3.7915e-05 1.0853e-03
Layer 1 1.0938e-02 1.6747e-01
WM 9.9976e-01 5.4847e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
RAC1 Expression Distribution
Gene Specificity Score (GSS)
RAC1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
RAC1 Layer 4 2.7715 0.7465
YWHAB Layer 4 2.8145 0.7440
GRIN1 Layer 4 2.9385 0.7420
YPEL3 Layer 4 2.9160 0.7407
STX1B Layer 4 3.1523 0.7405
STXBP1 Layer 4 2.8711 0.7403
CAMK2B Layer 4 2.6133 0.7396
TOMM20 Layer 4 2.7070 0.7347
ZNF483 Layer 4 2.9961 0.7342
SNCB Layer 4 2.6602 0.7341
MAPK8IP2 Layer 4 2.7334 0.7331
PNMA2 Layer 4 2.7910 0.7327
NPTX1 Layer 4 3.0195 0.7318
MEF2C Layer 4 2.9922 0.7316
GPI Layer 4 2.7422 0.7315
MORF4L2 Layer 4 3.0459 0.7296
ARL6IP1 Layer 4 2.7656 0.7290
PPP3CA Layer 4 2.7070 0.7288
NSF Layer 4 2.7939 0.7286
SCN2A Layer 4 2.5938 0.7283
SNRPN Layer 4 2.6777 0.7278
DMTN Layer 4 2.5996 0.7278
SERINC1 Layer 4 2.6016 0.7274
ATP6V0A1 Layer 4 2.8027 0.7268
CEND1 Layer 4 3.0254 0.7258
NDUFS5 Layer 4 2.5391 0.7258
MORF4L1 Layer 4 2.7910 0.7253
STMN1 Layer 4 2.6250 0.7253
RAB6B Layer 4 2.7305 0.7249
SIRPA Layer 4 3.0918 0.7235
CYFIP2 Layer 4 2.8027 0.7235
FAIM2 Layer 4 2.6016 0.7234
BASP1 Layer 4 2.6074 0.7230
ATP5MD Layer 4 2.5195 0.7229
SPTAN1 Layer 4 2.8770 0.7228
ATP5F1B Layer 4 2.4570 0.7220
UQCRH Layer 4 2.5635 0.7206
RPL14 Layer 4 2.6016 0.7197
UQCRB Layer 4 2.6543 0.7196
AP2M1 Layer 2 2.3242 0.7195
REEP5 Layer 4 2.8457 0.7191
HINT1 Layer 4 2.7480 0.7185
DDX24 Layer 4 3.0059 0.7185
NAPB Layer 4 2.7656 0.7184
YWHAG Layer 4 2.5723 0.7183
SOD2 Layer 4 2.8965 0.7183
GAS7 Layer 4 3.0312 0.7182
RNF11 Layer 4 2.5176 0.7182
SPRYD3 Layer 4 2.6455 0.7182
CSDE1 Layer 4 2.7822 0.7171

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1206
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1206_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1206/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1206/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1206/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1206/report/PD/BN1206_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1206/report/PD/BN1206_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 02:49:09
  • Number of Processes: 10
  • Spending Time: 0h 3m